3D Geometric Analysis of Tubular Objects based on Surface Normal Accumulation

This paper proposes a simple and efficient method for the reconstruction and extraction of geometric parameters from 3D tubular objects. Our method constructs an image that accumulates surface normal information, then peaks within this image are located by tracking. Finally, the positions of these are optimized to lie precisely on the tubular shape centerline. This method is very versatile, and is able to process various input data types like full or partial mesh acquired from 3D laser scans, 3D height map or discrete volumetric images. The proposed algorithm is simple to implement, contains few parameters and can be computed in linear time with respect to the number of surface faces. Since the extracted tube centerline is accurate, we are able to decompose the tube into rectilinear parts and torus-like parts. This is done with a new linear time 3D torus detection algorithm, which follows the same principle of a previous work on 2D arc circle recognition. Detailed experiments show the versatility, accuracy and robustness of our new method.Comment: in 18th International Conference on Image Analysis and Processing, Sep 2015, Genova, Italy. 201

Pearling: stroke segmentation with crusted pearl strings

We introduce a novel segmentation technique, called Pearling, for the semi-automatic extraction of idealized models of networks of strokes (variable width curves) in images. These networks may for example represent roads in an aerial photograph, vessels in a medical scan, or strokes in a drawing. The operator seeds the process by selecting representative areas of good (stroke interior) and bad colors. Then, the operator may either provide a rough trace through a particular path in the stroke graph or simply pick a starting point (seed) on a stroke and a direction of growth. Pearling computes in realtime the centerlines of the strokes, the bifurcations, and the thickness function along each stroke, hence producing a purified medial axis transform of a desired portion of the stroke graph. No prior segmentation or thresholding is required. Simple gestures may be used to trim or extend the selection or to add branches. The realtime performance and reliability of Pearling results from a novel disk-sampling approach, which traces the strokes by optimizing the positions and radii of a discrete series of disks (pearls) along the stroke. A continuous model is defined through subdivision. By design, the idealized pearl string model is slightly wider than necessary to ensure that it contains the stroke boundary. A narrower core model that fits inside the stroke is computed simultaneously. The difference between the pearl string and its core contains the boundary of the stroke and may be used to capture, compress, visualize, or analyze the raw image data along the stroke boundary

Extracting Vascular Networks under Physiological Constraints via Integer Programming

Abstract. We introduce an integer programming-based approach to vessel net-work extraction that enforces global physiological constraints on the vessel struc-ture and learn this prior from a high-resolution reference network. The method accounts for both image evidence and geometric relationships between vessels by formulating and solving an integer programming problem. Starting from an over-connected network, it is pruning vessel stumps and spurious connections by evaluating bifurcation angle and connectivity of the graph. We utilize a high-resolution micro computed tomography (µCT) dataset of a cerebrovascular corro-sion cast to obtain a reference network, perform experiments on micro magnetic resonance angiography (µMRA) images of mouse brains and discuss properties of the networks obtained under different tracking and pruning approaches.

On the Introduction of Automatic Program Repair in Bloomberg

A key to the success of Automatic Program Repair techniques is how easily they can be used in an industrial setting. In this article, we describe a collaboration by a team from four UK-based universities with Bloomberg (London) in implementing automatic, high-quality fixes to its code base. We explain the motivation for adopting APR, the mechanics of the prototype tool that was built, and the practicalities of integrating APR into existing systems. IEE

NetMets: software for quantifying and visualizing errors in biological network segmentation

One of the major goals in biomedical image processing is accurate segmentation of networks embedded in volumetric data sets. Biological networks are composed of a meshwork of thin filaments that span large volumes of tissue. Examples of these structures include neurons and microvasculature, which can take the form of both hierarchical trees and fully connected networks, depending on the imaging modality and resolution. Network function depends on both the geometric structure and connectivity. Therefore, there is considerable demand for algorithms that segment biological networks embedded in three-dimensional data. While a large number of tracking and segmentation algorithms have been published, most of these do not generalize well across data sets. One of the major reasons for the lack of general-purpose algorithms is the limited availability of metrics that can be used to quantitatively compare their effectiveness against a pre-constructed ground-truth. In this paper, we propose a robust metric for measuring and visualizing the differences between network models. Our algorithm takes into account both geometry and connectivity to measure network similarity. These metrics are then mapped back onto an explicit model for visualization

Alzheimer's Disease: a Review of its Visual System Neuropathology. Optical Coherence Tomography-a Potential Role As a Study Tool in Vivo

Alzheimer's disease (AD) is a prevalent, long-term progressive degenerative disorder with great social impact. It is currently thought that, in addition to neurodegeneration, vascular changes also play a role in the pathophysiology of the disease. Visual symptoms are frequent and are an early clinical manifestation; a number of psychophysiologic changes occur in visual function, including visual field defects, abnormal contrast sensitivity, abnormalities in color vision, depth perception deficits, and motion detection abnormalities. These visual changes were initially believed to be solely due to neurodegeneration in the posterior visual pathway. However, evidence from pathology studies in both animal models of AD and humans has demonstrated that neurodegeneration also takes place in the anterior visual pathway, with involvement of the retinal ganglion cells' (RGCs) dendrites, somata, and axons in the optic nerve. These studies additionally showed that patients with AD have changes in retinal and choroidal microvasculature. Pathology findings have been corroborated in in-vivo assessment of the retina and optic nerve head (ONH), as well as the retinal and choroidal vasculature. Optical coherence tomography (OCT) in particular has shown great utility in the assessment of these changes, and it may become a useful tool for early detection and monitoring disease progression in AD. The authors make a review of the current understanding of retinal and choroidal pathological changes in patients with AD, with particular focus on in-vivo evidence of retinal and choroidal neurodegenerative and microvascular changes using OCT technology.info:eu-repo/semantics/publishedVersio

Comparing algorithms for automated vessel segmentation in computed tomography scans of the lung: the VESSEL12 study

The VESSEL12 (VESsel SEgmentation in the Lung) challenge objectively compares the performance of different algorithms to identify vessels in thoracic computed tomography (CT) scans. Vessel segmentation is fundamental in computer aided processing of data generated by 3D imaging modalities. As manual vessel segmentation is prohibitively time consuming, any real world application requires some form of automation. Several approaches exist for automated vessel segmentation, but judging their relative merits is difficult due to a lack of standardized evaluation. We present an annotated reference dataset containing 20 CT scans and propose nine categories to perform a comprehensive evaluation of vessel segmentation algorithms from both academia and industry. Twenty algorithms participated in the VESSEL12 challenge, held at International Symposium on Biomedical Imaging (ISBI) 2012. All results have been published at the VESSEL12 website http://vessel12.grand-challenge.org. The challenge remains ongoing and open to new participants. Our three contributions are: (1) an annotated reference dataset available online for evaluation of new algorithms; (2) a quantitative scoring system for objective comparison of algorithms; and (3) performance analysis of the strengths and weaknesses of the various vessel segmentation methods in the presence of various lung diseases.Rudyanto, RD.; Kerkstra, S.; Van Rikxoort, EM.; Fetita, C.; Brillet, P.; Lefevre, C.; Xue, W.... (2014). Comparing algorithms for automated vessel segmentation in computed tomography scans of the lung: the VESSEL12 study. Medical Image Analysis. 18(7):1217-1232. doi:10.1016/j.media.2014.07.003S1217123218